Our lab identifies plant genes and investigates their functions. We are interested in genes involved in reproduction and development (the process by which a complex, multicellular plant develops from a single cell). We are also interested in the molecular evolution of the genes we study.

We are grateful for support from the National Science Foundation [www.nsf.gov] and for previous support from the USDA and W.J. Murdock Charitable Trust.

We do our research on a small weed, Arabidopsis thaliana, a member of the mustard family popular for research on plant genetics, genomics, and development. Like the human genome, the Arabidopsis genome has been the focus of a massive genome sequencing project, and its DNA has been completely sequenced, just like that of the human genome. Arabidopsis has therefore become one of a small, select group of model species that biologists focus on to identify genes and learn about genomes. Determining the functions all of this plant's genes, and figuring out how they work together to build and operate the plant, is now a major goal of plant biologists. Our work follows up on the Arabidopsis genome project by defining related groups of genes, determining their boundaries, surveying their expression, and investigating their functions. More detailed information on Arabidopsis and its genome is available at The Arabidopsis Information Resource (TAIR; http://www.arabidopsis.org/)

Arabidopsis thaliana: A model system for studies of plant biology. You gotta love it!

..Learning from knockout mutants: Top- photos of a mutant embryo (left) that has a gene called emb175 disrupted, compared to a normal Arabdiopsis embryo (shown inside of a seed). The mutant appears to just consist of a couple of disorganized blobs of cells, while the normal embryo has cotyledons (embryonic leaves) and other differentiated organs and tissues. The gene disrupted in this mutant is clearly essential early in the development of the plant embryo. Below is a map of the EMB175 gene, which we cloned and found encodes a PPR protein. The white rectangle labeled "T-DNA" represents a piece of foreign bacterial DNAwhich is lodged into this gene in the emb175 knockout mutant. Our research on emb175, and several other mutants with disrupted PPR genes, provided the first rigorous evidence that PPRs are crucial very early in plant development. (From Cushing et al., 2005)

As one strategy to figure out what different genes do, we study gene knock-out mutants. These are mutants in which a specific gene has been disrupted by insertion of a foreign piece of DNA. One can learn where a gene is active and what processes it is important for by observing what happens when it is screwed up.

We are working on mutants for two different kinds of genes. The first encodes Plant Intracellular Ras-group-related Leucine-rich repeat proteins (PIRLs), which are a familyof Leucine-Rich Repeat proteins found only in plants, but which are related to animal LRR proteins involved in gene regulation and cell signaling.

The second group of genes we study are Pentatricopeptide Repeat (PPR) genes, many of which encode proteins that act in post-transcriptional steps of gene expression in organelles (plastids and mitochondria). We work on a sub-set of PPR genes that are essential for embryogenesis. Much of our past research was also on plant embryo development.

Our lab is at Whitman College, and Whitman undergraduate students make important contributions to the research. The Publication, C.V., and Team Weed links here (or above) lead to more information on our research and members of the lab. Some representative examples of research findings & topics are shown below, with links to corresponding publications.

RESEARCH NUGGETS: SOME PHOTOS & FINDINGS FROM VARIOUS PROJECTS

The roles of PPR genes in plant embryogenesisThese photos show developing embryos from different ppr gene knock-out mutants, exhibiting weird and diverse morphological defects. These mutants, along with emb175 (shown above) demonstrated that inactivation of PPR genes can cause diverse and severe defects in embryo morphogenesis. The PPR proteins encoded by these genes may influence embryo morphology directly, or indirectly, through their activity in organelle gene expression (From Cushing et al., 2005)

..Gene Discovery: PIRLs, a novel class of LRR genes Top: A diagram of the PIRL1 gene and mRNA structures, showing positions of introns (red) and exons. PIRL1 is one of a family of 9 Arabidopsis genes we have identified. PIRLs encode Leucine-Rich Repeat (LRR) proteins related to animal LRR proteins involved in cell signal transduction. "PIRL" stands for "Plant Intracellular Ras-group-related LRR". [PIRLs are described in Forsthoefel et al, 2005].Bottom: Pollen from plants containing knockout mutations in two related PIRL genes. On left, an abnormal mutant pollen, compared to a normal pollen grain (stained purple) with at least one of the genes intact. On the right is a scanning electron microscope photo of a wrinkly, pathetic double-mutant pollen grain. These sorts of results have shown us that these 2 related PIRL genes are needed for pollen development. Current research, supported by the NSF, is focused on those genes [Summarized in abstracts by Forsthoefel et al. 2006, 2008, & 2009; reported in Forsthoefel et al, 2010].

Genome Evolution: massive expansion of the PPR superfamily in higher plantsGraphs comparing intron numbers for PPR genes (on left) to a set of control genes of similar size (right). Most PPR genes have no introns. This is part of our ongoing study of PPR gene evolution. PPR genes are found in all eukaryotes (plants, animals, fungi, etc) but in plants they are one of the biggest classes of genes. (Arabidopsis has >400 PPR-encoding genes). How did this family expand so much in plants? Our hypothesis is that early in plant evolution, PPRs multiplied via RNA intermediates: they got transcribed to RNA, then reverse-transcribed back into DNA and re-inserted into the genome. One hallmark of this type of gene duplication is genes that lack introns, since introns are removed from RNA just after transcription. [Anderson et al, 2004]

Maintenance of differentiated cell identity in embryogenesis
The photos above show twin embryos developing within single seeds from the Arabidopsis twin1 mutant. Second embryos form from a column of cells called the suspensor, which in normal embryos degenerates and disappears late in embryo development. This mutant phenotype showed that the TWIN1 gene is required to maintain suspensor cell identity in the developing embryo. It also showed that in plants, loss of a single gene can cause embryogenic transformation of what should be a differentiated cell type. (From Vernon and Meinke, 1994; work done w/ Dr. David Meinke at OSU ).

Chromosomal translocations in T-DNA mutagenesis: Implications for Functional Genomics and Genetics
Above is a map of a large chromosomal translocation associated with a T-DNA insert, which we identified in the Arabidopsis emb88 mutant. T-DNA, a fragment of DNA from Agrobacterium, normally inserts cleanly into plant chromosomes, where it can interrupt genes. Therefore it is frequently used as a mutagen to make gene knockout mutants, which are used to research gene functions.
Here, a large chunk of Arabidopsis chromosome 5 (shown in yellow & gray) was found adjacent to a T-DNA (blue) lodged into chromosome 1 (red), at the emb88 mutant locus. Thousands of T-DNA knock-out mutatns are now being studied by scores of labs all over the world. This work demonstated that Arabidopsis knock-out lines can contain weird chromosomal abnormalities that may interfere with such functional genomic studies. [Described in Tax and Vernon, 2001]

Regulation of embryo morphology and organ patterning
The above photographs show examples of twin1 mutant seedlings with abnormal cotyledon patterning and morphology. Panel 1 shows a wild-type Arabidopsis seedling, with 2 identical cotyledons (specialized leaves that form during embryogenesis). Panels 2-6 show various twin1 mutant seedlings with single, fused, or triple cotyledons. These results showed that the TWIN1 gene is important for proper organ patterning at the embryonic shoot apex, as well its previously defined function in the developing embryo. (From Vernon et al., 2001)